{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"submitter":["Anne Stringer"],"instrument_platform":["not applicable","Illumina HiSeq 1000"],"study_type":["DNA-seq"],"organism":["Salmonella enterica subsp. enterica"],"species":["Salmonella enterica subsp. enterica"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16844"],"description":["Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S CRISPRi library, growth with and without bile salts."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sequencing - Sequencing was performed on an Illumina Next-Seq Instrument (Wadsworth Center Applied Genomics Technologies Core).","Sample Treatment - Cells are resuspended in LB + 100mM  MOPS + 100ug/mL ampicillin, with or without 3% bile salt treatment. (sodium choleate, SIGMA S9875)","Sample Treatment - no treatment","Sample Collection - Sample collection and nucleic acid purification happen in the same step. After setting up initial culture, miniprep remaining cells from thawed aliquot (= \\\"start\\\").  Use Qiagen Spin Miniprep Kit -include Buffer PB wash, elute in 30 uL water.  After 4.5 hrs growth and dilute to OD600=0.01, take 1.2 mL of culture and miniprep (same miniprep procedure) (= \\\"set 1\\\").  After 4.5 hrs growth, take 1.2 mL of culture and miniprep (same miniprep protocol) (= \\\"set 2\\\").  Qubit quantify all minipreps. Start and set 2 sample used for this experiment.","Growth Protocol - Thaw glycerol stocks pAMD240 and pAMD241.  Mix gently.  Add 250 uL each glycerol stock to 12.5 mL LB+amp.  Measure OD600.  Dilute again 1 mL culture in 12.5 mL LB+amp.  Record OD600.  Grow o/n at 37deg/225 rpm.  Next day set up 200 uL aliquots of cells + 50 uL 50% glycerol and flash freeze on dry ice.  Thaw aliquot of frozen cells from \\\"14028s CRISPRi culture setup\\\" protocol.  Dilute cells to OD600=0.01 (4 mL volume).  Grow 4.5 hours at 37deg/225 rpm.  Dilute to OD600=0.01 (4 mL volume).  Grow 4.5 hours at 37deg/225 rpm.","Library Construction - use 20 ng of miniprepped DNA (from \\\"miniprep\\\" sample extraction protocol) as template for PCR.  Set up 4 x 50 uL PCR for each sample using Taq. Final concentration ultramers = 0.1 uM.  Cycling:  initial denaturation 95deg - 5 min; 10 cycles of 95deg-30 sec, 53deg-40sec, 68deg-1min; final extension 68deg-5 min; 4deg hold.  Combine like PCRs and run 15 uL on acrylamide gel, 110V, 75min.  Divide remaining PCR sample into 2 tubes and AMPure 0.8x clean.  Elute each in 30 uL water, combine like samples, AMPure 0.8x clean again.  Elute 11 uL. Qubit quantify.","Growth Protocol - Thaw glycerol stock pAMD241 (14028s dCas3::thyA  + Salmonella CRISPRi library).  Mix gently.  Add 250 uL each glycerol stock to 12.5 mL LB+ 100ug/mL ampicillin. Measure OD600.  Dilute again 1 mL culture in 12.5 mL LB+/mL ampicillin,  Record OD600.  Grow o/n at 37deg/225 rpm.  Next day set up 200 uL aliquots of cells + 50 uL 50% glycerol and flash freeze on dry ice.     For experiment, thaw 3 aliquots frozen cells. Wash 2x in water, resuspend in 190 ul LB + 100mM MOPS + 100ug/mL ampicillin. Add 18.7 ul cells to 4 mL LB + 100mM MOPS + 100ug/mL ampicillin and add to 4mL LB + 100mM MOPS + 100ug/mL ampicillin + 3% bile salts.  Grow 4.5 hours at 37C/225 rpm.  Miniprep cells for “set1”. Dilute to OD600=0.01 (4 mL volume).  Grow 4.5 hours at 37C/225 rpm. Miniprep cells for “set2”. Miniprep remaining cells form frozen aliquot for “start”","Nucleic Acid Extraction - After setting up initial culture, miniprep remaining cells from thawed aliquot (= \\\"start\\\").  Use Qiagen Spin Miniprep Kit -include Buffer PB wash, elute in 30 uL water.  After 4.5 hrs growth and dilute to OD600=0.01, take 1.2 mL of culture and miniprep (same miniprep procedure) (= \\\"set 1\\\").  After 4.5 hrs growth, take 1.2 mL of culture and miniprep (same miniprep protocol) (= \\\"set 2\\\").  Qubit quantify all minipreps. Start and set 2 sample used for this experiment."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","MAGE-TAB Files"],"pubmed_authors":["Anne Stringer"],"additional_accession":[]},"is_claimable":false,"name":"14028s CRISPRi Bile salts","description":"Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S CRISPRi library, growth with and without bile salts.","dates":{"release":"2026-04-15T00:00:00Z","modification":"2026-04-17T01:01:34.054Z","creation":"2026-04-01T11:16:39.584Z"},"accession":"E-MTAB-16844","cross_references":{"ENA":["ERP191665"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0002693","EFO_0005518","EFO_0004184","EFO_0003969"]}}